[gmx-users] residue number starting from not 1
Hi all, My system contains water (SOL) + polyelectrolyte (PSS with DP 30) + sodium ions (Na). Before the EM, I have run editconf -f -noc -resnr 1 -o to set the resnr. After the EM, the resnr becomes wrong. But the atomnr is still correct. 1. the resnr of the first water starting from DP+1, not 1. (I have checked some other systems with DP=15 or DP=12) 2. the resnr of the first PSS residue on the ALL the PSS chain starts from 1, but not the resnr(of previous water/PSS residue) +1. 3. the resnr of the first Na residue is the resnr(of the last water residue) +1, but not the resnr(of the previous PSS residue) +1 It seems that the problem is caused from the polymer. Any comment or suggestion is sincerely welcome! Gromacs 4.5.3 0.1MNaCl + DP30 380329 31SOL OW1 4.323 10.990 14.598 -0.2147 0.1640 -0.0659 31SOLHW12 4.280 11.043 14.525 -0.8319 3.1315 2.3305 31SOLHW23 4.253 10.953 14.659 0.3787 -0.3030 0.3439 32SOL OW4 0.863 3.787 10.720 0.8624 -0.6556 0.5765 32SOLHW15 0.785 3.827 10.671 1.9981 0.4779 -0.3465 32SOLHW26 0.904 3.716 10.663 0.9971 -0.6900 0.7175 .. 99316SOL OW97856 0.834 8.769 22.747 -0.2436 -0.7048 0.2608 99316SOLHW197857 0.931 8.745 22.754 -0.0076 0.0674 -0.2549 99316SOLHW297858 0.819 8.860 22.787 -0.9561 -1.2962 1.3663 1PSSCAA97859 9.971 3.747 8.913 0.0608 -0.0677 -0.0792 1PSS HAA197860 9.949 3.849 8.936 0.1767 -0.4602 1.7875 . 30PSS HAB298430 8.204 6.232 10.780 0.9449 -0.2721 0.7855 1PSSCAA98431 1.197 5.317 19.589 -0.1509 -0.1143 -0.2474 . 30PSS HAB299002 1.549 1.832 20.579 1.3918 3.3370 1.4906 1PSSCAA99003 5.657 5.376 6.520 -0.1073 -0.0351 -0.8729 ... 30PSS HAB2 9298 3.526 0.458 16.652 -1.6044 1.1441 1.3393 99317Na Na 9299 12.146 5.676 14.924 -0.1802 -0.9861 0.2229 99318Na Na 9300 11.363 11.645 8.887 0.4524 -0.4644 -0.0401 ... .. regards, Baofu Qiao -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_msd capabilities
Is it possible to calculate of a solute in a binary mixture, in order to obtain Maxwell-Stefan diffusion coefficient, using g_msd from Gromacs? Luís Martinsclip_image002.png-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_msd mutual diffusion coefficient
Dear colleagues I'd like to know if it is possible to calculate of a solute in a binary mixture, in order to obtain Maxwell-Stefan diffusion coefficient, using g_msd from Gromacs. Can anyone tell something about that? Thanks Best regards Luís Martins -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] To get PMF using pull geometry of cylinder
Thank you Justin. But I'm still confused about the pull_vec1. Is the vector pointing from the reference or from the pull group for all the geometry settings? For instance, if I use pull_geometry = position, pull_dim = N N Y, pull_rate1 = 0.1, pull_init1 = 3.0, pull_vec1 = 0 0 1, the position = pull_init + time*pull_rate*pull_vec1 according to the manual and it's actually pulling the pull group away from the reference because the vector has a positive z component. BTW, I did consider using position geometry but can I get the PMF using pull_rate NOT equal to zero? The reason I turned to cylinder is that with distance geometry the membrane concaved as the micelle was restrained to a very short distance (any distance below the critical distance where the fusion was supposed to occur) without fusing and this would persist for some hundred nanoseconds. Thanks again for your help! Dejun From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Wednesday, May 25, 2011 7:44 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] To get PMF using pull geometry of cylinder Lin, Dejun wrote: Hi all, I want to do an umbrella sampling to calculate the potential of mean force of a micelle fusing to a lipid membrane. In the starting configuration, the membrane normal is set in z direction and the membrane is under the micelle (z(COM-membrane) z(COM-micelle)). At the beginning, I used pull_geometry = distance but the sampling took to long to converge. And then I considered using cylinder instead and set up the pull code as: pull = umbrella pull_geometry = cylinder pull_dim = N N Y pull_start = no pull_ngroups = 1 pull_group0 = membrane pull_group1 = micelle pull_vec1 = 0.0 0.0 -1.0 pull_r1 = 2.3 pull_r0 = 2.5 pull_init1= 1.8 pull_rate1= 0.0 pull_k1 = 1000 pull_nstxout = 1000 pull_nstfout = 1000 And the output files (px.xvg and pf.xvg) look like: (px.xvg) 0. 23.3397 4.90267 100. 0.7424261.86002 200. 0.7378421.86232 300. 0.7626411.83985 400. 21.6814 1.86777 500.0.771017 1.82482 600. 0.7890361.83254 700. 0.7937451.83503 800. 0.804732 1.84217 900.0.80137 1.84166 1000. 0.8179791.83546 1100. 0.8062721.83535 1200. 0.792355 1.80372 1300. 0.786839 1.8438 1400. 0.7986861.82625 1500. 0.8028591.84138 1600. 0.803844 1.84379 (pf.xvg) 100. -480.158 200. -498.547 300. -318.839 400. -542.14 500. -198.526 600. -260.291 700. -280.22 800. -337.385 900. -333.317 1000. -283.644 1100. -282.761 1200. -29.7684 1300.-350.409 1400. -209.991 1500. -331.029 1600. -350.309 And I visualized the trajectory in VMD and found that an explosion of the micelle (with all its residues scattered in the box). I then changed the pull_vec1 = 0.0 0.0 -1.0 to pull_vec1 = 0.0 0.0 1.0 and the explosion was gone and everything seemed to work. But I'm not quite sure if I'm setting up the pull-code right because if z(COM-membrane) z(COM-micelle), then pull_vec1 = 0.0 0.0 -1.0 should be the right choice. Basically, I think my The negative is incorrect. If the micelle is above the membrane (i.e., it has a greater z-coordinate), then the reference vector should be positive with respect to the reference position. It would appear from the pullx.xvg file that you've got some weird PBC crossing going on, since the reference positions oscillate dramatically at the beginning of the simulation. pull-code is restraining the COM of the micelle to the COM of a cylinder of the membrane at a distance of 1.8nm, with the vector pointing from COM(micelle) to COM(cylinder) being (0,0,-1). So can anyone explain what caused the explosion or am I setting up the pull-code right? And what are the 2nd and 3rd column in the px.xvg output in this case? For such a simple restraint, I don't think there is any need for cylinder geometry. You're not using different weighting. Any of the other pull_geometry settings should work, with distance probably being the most intuitive. I suspect it would be very easy to use the position setting as well. The output in the pullx.xvg file should be labeled in the header. The generic output is (x,y,z) of the reference group, followed by delta(x,y,z) for the restrained group,
RE: [gmx-users] To get PMF using pull geometry of cylinder
Ah...Sorry if I confused you. Actually what I meant is if I set the pull code, e.g., as: pull_geometry = position pull_dim = N N Y pull_rate1 = 0.1 pull_init1 = 3.0 pull_vec1 = 0 0 1 (where pull rate is NOT zero) Then the position = pull_init + time*pull_rate*pull_vec1 and since pull_vec1 is z-component-positive (0, 0, 1), the position between the reference and the pull group increases monotonically and that's not what I want. I want the distance to decrease so the pull_vec1 should be (0,0,-1). Am I right? Thanks, Dejun From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Thursday, May 26, 2011 11:26 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] To get PMF using pull geometry of cylinder Lin, Dejun wrote: Thank you Justin. But I'm still confused about the pull_vec1. Is the vector pointing from the reference or from the pull group for all the geometry settings? For instance, if I use pull_geometry = position, pull_dim = N N Y, pull_rate1 = 0.1, pull_init1 = 3.0, pull_vec1 = 0 0 1, the position = pull_init + time*pull_rate*pull_vec1 according to the manual and it's actually pulling the pull group away from the reference because the vector has a positive z component. The reference group serves as the reference :) Thus, the vector connecting your reference and pull group is (0,0,1) since the pull group has a larger z-coordinate. You're right about the position equation, but you've got a pull_rate1 of zero, so the added term drops out and position = pull_init1. BTW, I did consider using position geometry but can I get the PMF using pull_rate NOT equal to zero? The reason I turned to cylinder is that with distance geometry the membrane concaved as the micelle was restrained to a very short distance (any distance below the critical distance where the fusion was supposed to occur) without fusing and this would persist for some hundred nanoseconds. To obtain the PMF, the pull rate should be zero, using several (many) independent simulations along the desired reaction coordinate. See the tutorial: http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling -Justin Thanks again for your help! Dejun From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Wednesday, May 25, 2011 7:44 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] To get PMF using pull geometry of cylinder Lin, Dejun wrote: Hi all, I want to do an umbrella sampling to calculate the potential of mean force of a micelle fusing to a lipid membrane. In the starting configuration, the membrane normal is set in z direction and the membrane is under the micelle (z(COM-membrane) z(COM-micelle)). At the beginning, I used pull_geometry = distance but the sampling took to long to converge. And then I considered using cylinder instead and set up the pull code as: pull = umbrella pull_geometry = cylinder pull_dim = N N Y pull_start = no pull_ngroups = 1 pull_group0 = membrane pull_group1 = micelle pull_vec1 = 0.0 0.0 -1.0 pull_r1 = 2.3 pull_r0 = 2.5 pull_init1 = 1.8 pull_rate1= 0.0 pull_k1 = 1000 pull_nstxout = 1000 pull_nstfout = 1000 And the output files (px.xvg and pf.xvg) look like: (px.xvg) 0. 23.3397 4.90267 100. 0.7424261.86002 200.0.7378421.86232 300. 0.7626411.83985 400.21.6814 1.86777 500.0.771017 1.82482 600. 0.7890361.83254 700.0.793745 1.83503 800. 0.804732 1.84217 900. 0.80137 1.84166 1000. 0.8179791.83546 1100. 0.8062721.83535 1200. 0.792355 1.80372 1300. 0.786839 1.8438 1400. 0.798686 1.82625 1500. 0.8028591.84138 1600. 0.803844 1.84379 (pf.xvg) 100. -480.158 200. -498.547 300. -318.839 400. -542.14 500. -198.526 600. -260.291 700. -280.22 800. -337.385 900. -333.317 1000. -283.644 1100. -282.761 1200. -29.7684 1300.-350.409 1400. -209.991 1500. -331.029 1600. -350.309 And I visualized the trajectory in VMD and found that an explosion of the micelle (with all its residues scattered in the box). I then changed the pull_vec1 = 0.0 0.0 -1.0 to pull_vec1 = 0.0 0.0 1.0 and the explosion was gone and everything seemed to work. But I'm not quite sure if I'm setting up the pull-code right because if z(COM-membrane) z(COM-micelle), then pull_vec1 = 0.0 0.0 -1.0 should be the right
Re: [gmx-users] electron density
dear all, regarding the matter of electron density, can anyone clarify me on the output units? from this discussion i understand the values are presented in electrons/A^3 - is this correct? best regards, igor Igor Marques Molecular Modeling Group – Univ. of Aveiro http://molecular-modeling.dq.ua.pt/ On Sat, Jan 1, 2011 at 9:01 PM, Jianhui Tian jianhuit...@gmail.com wrote: Problem solved. The 2 in the text is just a typo when I sent the email. So actually there is no partial charge in the electrons.dat file. Thanks, Justin. Jianhui Date: Sat, 01 Jan 2011 13:56:45 -0500 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] electron density To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4d1f78ed.5070...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Jianhui Tian wrote: Date: Fri, 31 Dec 2010 19:08:50 -0500 From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu Subject: Re: [gmx-users] electron density To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 4d1e7092.7060...@vt.edu mailto:4d1e7092.7060...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Jianhui Tian wrote: Hi gmx users, I tried to calculate both the mass density and electron density for the water layer of a membrane simulation. The mass density is 1000 kg/m^3, however the electron density I got is smaller than about 0.33 e/A^3. I How much smaller? I got about 0.27 e/A^3. am using a CHARMM force field and the CHARMM version of TIP3P water. Am I doing anything wrong when calculating the electron density? Thanks a lot. Possibly, but without seeing what you used for input, information about your simulation, etc it's impossible to say. In the electrons.dat file, I had 2 OW = 8.834 HW1 = 0.583 HW2 = 0.583 And then used g_density ... -ei electrons.dat -dens electron ... There are several problems. The first line of electrons.dat indicates there are only two unique atom names, but clearly you're supplying three. Second, this file is read in such that at integral number of electrons is detected on each line. So, in your case, two lines are being read, one that detects 8 electrons, and another that detects zero. -Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] To get PMF using pull geometry of cylinder
Lin, Dejun wrote: Ah...Sorry if I confused you. Actually what I meant is if I set the pull code, e.g., as: pull_geometry = position pull_dim = N N Y pull_rate1 = 0.1 pull_init1 = 3.0 pull_vec1 = 0 0 1 (where pull rate is NOT zero) Then the position = pull_init + time*pull_rate*pull_vec1 and since pull_vec1 is z-component-positive (0, 0, 1), the position between the reference and the pull group increases monotonically and that's not what I want. I want the distance to decrease so the pull_vec1 should be (0,0,-1). Am I right? If you want the two species to approach rather than separate, do not change the pull_vec, change the pull_rate so that it is less than zero. A negative pull_rate will decrease the separation over time. Note that pull_dim is irrelevant for pull_geometry=position; only pull_vec1 is required. -Justin Thanks, Dejun From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Thursday, May 26, 2011 11:26 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] To get PMF using pull geometry of cylinder Lin, Dejun wrote: Thank you Justin. But I'm still confused about the pull_vec1. Is the vector pointing from the reference or from the pull group for all the geometry settings? For instance, if I use pull_geometry = position, pull_dim = N N Y, pull_rate1 = 0.1, pull_init1 = 3.0, pull_vec1 = 0 0 1, the position = pull_init + time*pull_rate*pull_vec1 according to the manual and it's actually pulling the pull group away from the reference because the vector has a positive z component. The reference group serves as the reference :) Thus, the vector connecting your reference and pull group is (0,0,1) since the pull group has a larger z-coordinate. You're right about the position equation, but you've got a pull_rate1 of zero, so the added term drops out and position = pull_init1. BTW, I did consider using position geometry but can I get the PMF using pull_rate NOT equal to zero? The reason I turned to cylinder is that with distance geometry the membrane concaved as the micelle was restrained to a very short distance (any distance below the critical distance where the fusion was supposed to occur) without fusing and this would persist for some hundred nanoseconds. To obtain the PMF, the pull rate should be zero, using several (many) independent simulations along the desired reaction coordinate. See the tutorial: http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling -Justin Thanks again for your help! Dejun From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Wednesday, May 25, 2011 7:44 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] To get PMF using pull geometry of cylinder Lin, Dejun wrote: Hi all, I want to do an umbrella sampling to calculate the potential of mean force of a micelle fusing to a lipid membrane. In the starting configuration, the membrane normal is set in z direction and the membrane is under the micelle (z(COM-membrane) z(COM-micelle)). At the beginning, I used pull_geometry = distance but the sampling took to long to converge. And then I considered using cylinder instead and set up the pull code as: pull = umbrella pull_geometry = cylinder pull_dim = N N Y pull_start = no pull_ngroups = 1 pull_group0 = membrane pull_group1 = micelle pull_vec1 = 0.0 0.0 -1.0 pull_r1 = 2.3 pull_r0 = 2.5 pull_init1 = 1.8 pull_rate1= 0.0 pull_k1 = 1000 pull_nstxout = 1000 pull_nstfout = 1000 And the output files (px.xvg and pf.xvg) look like: (px.xvg) 0. 23.3397 4.90267 100. 0.7424261.86002 200.0.7378421.86232 300. 0.7626411.83985 400.21.6814 1.86777 500.0.771017 1.82482 600. 0.7890361.83254 700.0.793745 1.83503 800. 0.804732 1.84217 900. 0.80137 1.84166 1000. 0.8179791.83546 1100. 0.8062721.83535 1200. 0.792355 1.80372 1300. 0.786839 1.8438 1400. 0.798686 1.82625 1500. 0.8028591.84138 1600. 0.803844 1.84379 (pf.xvg) 100. -480.158 200. -498.547 300. -318.839 400. -542.14 500. -198.526 600. -260.291 700. -280.22 800. -337.385 900. -333.317 1000. -283.644 1100. -282.761 1200. -29.7684 1300.-350.409 1400. -209.991 1500. -331.029 1600. -350.309 And I visualized the trajectory in VMD and found that an explosion of the micelle (with all its residues scattered in the box). I then
[gmx-users] Re: Error of installing gromacs v4.5.4
Hi, Thank you for your reply. I'm not so good in computer. I think the platform you ask me is Linux, and kernel is 2.4.21-60.ELsmp The compiler is gcc v3.2.3 in the machine in my institute. Sincerely yours, Hsin-Lin Message: 1 Date: Thu, 26 May 2011 18:03:09 +0200 From: Szil?rd P?ll szilard.p...@cbr.su.se Subject: Re: [gmx-users] Error of installing gromacs v4.5.4 To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: BANLkTi=9v3+1dnbjsmd6hna-ayfdprb...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi Hsin-Lin, Your problem are caused by a missing header file which is included by the nobonded SSE kernels which is indicated by the first error in your output: nb_kernel400_ia32_sse.c:22:23: emmintrin.h: No such file or directory This header is needed for SSE and SSE2, but for some reason you don't have it. What platform are you compiling on/for and what compiler are you using? Alternatively, you can turn off acceleration and you'll be able to compile the code, but it will run *much* slower than with the accelerated kernels. -- Szil嫫d -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] electron density
Igor Marques wrote: dear all, regarding the matter of electron density, can anyone clarify me on the output units? from this discussion i understand the values are presented in electrons/A^3 - is this correct? No. It is electrons/nm^3. Standard units are defined in Chapter 2 of the manual (and printed in the code, of course). -Justin best regards, igor Igor Marques Molecular Modeling Group – Univ. of Aveiro http://molecular-modeling.dq.ua.pt/ On Sat, Jan 1, 2011 at 9:01 PM, Jianhui Tian jianhuit...@gmail.com mailto:jianhuit...@gmail.com wrote: Problem solved. The 2 in the text is just a typo when I sent the email. So actually there is no partial charge in the electrons.dat file. Thanks, Justin. Jianhui Date: Sat, 01 Jan 2011 13:56:45 -0500 From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu Subject: Re: [gmx-users] electron density To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 4d1f78ed.5070...@vt.edu mailto:4d1f78ed.5070...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Jianhui Tian wrote: Date: Fri, 31 Dec 2010 19:08:50 -0500 From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu Subject: Re: [gmx-users] electron density To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 4d1e7092.7060...@vt.edu mailto:4d1e7092.7060...@vt.edu mailto:4d1e7092.7060...@vt.edu mailto:4d1e7092.7060...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Jianhui Tian wrote: Hi gmx users, I tried to calculate both the mass density and electron density for the water layer of a membrane simulation. The mass density is 1000 kg/m^3, however the electron density I got is smaller than about 0.33 e/A^3. I How much smaller? I got about 0.27 e/A^3. am using a CHARMM force field and the CHARMM version of TIP3P water. Am I doing anything wrong when calculating the electron density? Thanks a lot. Possibly, but without seeing what you used for input, information about your simulation, etc it's impossible to say. In the electrons.dat file, I had 2 OW = 8.834 HW1 = 0.583 HW2 = 0.583 And then used g_density ... -ei electrons.dat -dens electron ... There are several problems. The first line of electrons.dat indicates there are only two unique atom names, but clearly you're supplying three. Second, this file is read in such that at integral number of electrons is detected on each line. So, in your case, two lines are being read, one that detects 8 electrons, and another that detects zero. -Justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Error of installing gromacs v4.5.4
Hsin-Lin Chiang wrote: Hi, Thank you for your reply. I'm not so good in computer. I think the platform you ask me is Linux, and kernel is 2.4.21-60.ELsmp The compiler is gcc v3.2.3 in the machine in my institute. The hardware specs are more significant here. cat /proc/cpuinfo should provide the necessary information. The exact configuration command you used would also be useful. Note that gcc 3.2.3 is extremely old, and often times new code will not compile properly with old compilers. You should upgrade gcc to something more modern. Surely your system has a package manager that can upgrade such components. -Justin Sincerely yours, Hsin-Lin Message: 1 Date: Thu, 26 May 2011 18:03:09 +0200 From: Szil?rd P?ll szilard.p...@cbr.su.se Subject: Re: [gmx-users] Error of installing gromacs v4.5.4 To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: BANLkTi=9v3+1dnbjsmd6hna-ayfdprb...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi Hsin-Lin, Your problem are caused by a missing header file which is included by the nobonded SSE kernels which is indicated by the first error in your output: nb_kernel400_ia32_sse.c:22:23: emmintrin.h: No such file or directory This header is needed for SSE and SSE2, but for some reason you don't have it. What platform are you compiling on/for and what compiler are you using? Alternatively, you can turn off acceleration and you'll be able to compile the code, but it will run *much* slower than with the accelerated kernels. -- Szil嫫d -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] To get PMF using pull geometry of cylinder
I see. That makes things clear. Thank you so much! -Dejun From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Thursday, May 26, 2011 1:09 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] To get PMF using pull geometry of cylinder Lin, Dejun wrote: Ah...Sorry if I confused you. Actually what I meant is if I set the pull code, e.g., as: pull_geometry = position pull_dim = N N Y pull_rate1 = 0.1 pull_init1 = 3.0 pull_vec1 = 0 0 1 (where pull rate is NOT zero) Then the position = pull_init + time*pull_rate*pull_vec1 and since pull_vec1 is z-component-positive (0, 0, 1), the position between the reference and the pull group increases monotonically and that's not what I want. I want the distance to decrease so the pull_vec1 should be (0,0,-1). Am I right? If you want the two species to approach rather than separate, do not change the pull_vec, change the pull_rate so that it is less than zero. A negative pull_rate will decrease the separation over time. Note that pull_dim is irrelevant for pull_geometry=position; only pull_vec1 is required. -Justin Thanks, Dejun From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Thursday, May 26, 2011 11:26 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] To get PMF using pull geometry of cylinder Lin, Dejun wrote: Thank you Justin. But I'm still confused about the pull_vec1. Is the vector pointing from the reference or from the pull group for all the geometry settings? For instance, if I use pull_geometry = position, pull_dim = N N Y, pull_rate1 = 0.1, pull_init1 = 3.0, pull_vec1 = 0 0 1, the position = pull_init + time*pull_rate*pull_vec1 according to the manual and it's actually pulling the pull group away from the reference because the vector has a positive z component. The reference group serves as the reference :) Thus, the vector connecting your reference and pull group is (0,0,1) since the pull group has a larger z-coordinate. You're right about the position equation, but you've got a pull_rate1 of zero, so the added term drops out and position = pull_init1. BTW, I did consider using position geometry but can I get the PMF using pull_rate NOT equal to zero? The reason I turned to cylinder is that with distance geometry the membrane concaved as the micelle was restrained to a very short distance (any distance below the critical distance where the fusion was supposed to occur) without fusing and this would persist for some hundred nanoseconds. To obtain the PMF, the pull rate should be zero, using several (many) independent simulations along the desired reaction coordinate. See the tutorial: http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling -Justin Thanks again for your help! Dejun From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Wednesday, May 25, 2011 7:44 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] To get PMF using pull geometry of cylinder Lin, Dejun wrote: Hi all, I want to do an umbrella sampling to calculate the potential of mean force of a micelle fusing to a lipid membrane. In the starting configuration, the membrane normal is set in z direction and the membrane is under the micelle (z(COM-membrane) z(COM-micelle)). At the beginning, I used pull_geometry = distance but the sampling took to long to converge. And then I considered using cylinder instead and set up the pull code as: pull = umbrella pull_geometry = cylinder pull_dim = N N Y pull_start = no pull_ngroups = 1 pull_group0 = membrane pull_group1 = micelle pull_vec1 = 0.0 0.0 -1.0 pull_r1 = 2.3 pull_r0 = 2.5 pull_init1 = 1.8 pull_rate1= 0.0 pull_k1 = 1000 pull_nstxout = 1000 pull_nstfout = 1000 And the output files (px.xvg and pf.xvg) look like: (px.xvg) 0. 23.3397 4.90267 100. 0.7424261.86002 200.0.7378421.86232 300. 0.7626411.83985 400.21.6814 1.86777 500.0.771017 1.82482 600. 0.7890361.83254 700.0.793745 1.83503 800. 0.804732 1.84217 900. 0.80137 1.84166 1000. 0.8179791.83546 1100. 0.8062721.83535 1200. 0.792355 1.80372 1300. 0.786839 1.8438 1400. 0.798686 1.82625 1500. 0.8028591.84138 1600. 0.803844 1.84379 (pf.xvg) 100. -480.158 200. -498.547 300. -318.839 400.
Re: [gmx-users] electron density
thanks mate! Igor Marques On Thu, May 26, 2011 at 6:12 PM, Justin A. Lemkul jalem...@vt.edu wrote: Igor Marques wrote: dear all, regarding the matter of electron density, can anyone clarify me on the output units? from this discussion i understand the values are presented in electrons/A^3 - is this correct? No. It is electrons/nm^3. Standard units are defined in Chapter 2 of the manual (and printed in the code, of course). -Justin best regards, igor Igor Marques Molecular Modeling Group – Univ. of Aveiro http://molecular-modeling.dq.ua.pt/ On Sat, Jan 1, 2011 at 9:01 PM, Jianhui Tian jianhuit...@gmail.commailto: jianhuit...@gmail.com wrote: Problem solved. The 2 in the text is just a typo when I sent the email. So actually there is no partial charge in the electrons.dat file. Thanks, Justin. Jianhui Date: Sat, 01 Jan 2011 13:56:45 -0500 From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu Subject: Re: [gmx-users] electron density To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 4d1f78ed.5070...@vt.edu mailto:4d1f78ed.5070...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Jianhui Tian wrote: Date: Fri, 31 Dec 2010 19:08:50 -0500 From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu Subject: Re: [gmx-users] electron density To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 4d1e7092.7060...@vt.edu mailto:4d1e7092.7060...@vt.edu mailto:4d1e7092.7060...@vt.edu mailto:4d1e7092.7060...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Jianhui Tian wrote: Hi gmx users, I tried to calculate both the mass density and electron density for the water layer of a membrane simulation. The mass density is 1000 kg/m^3, however the electron density I got is smaller than about 0.33 e/A^3. I How much smaller? I got about 0.27 e/A^3. am using a CHARMM force field and the CHARMM version of TIP3P water. Am I doing anything wrong when calculating the electron density? Thanks a lot. Possibly, but without seeing what you used for input, information about your simulation, etc it's impossible to say. In the electrons.dat file, I had 2 OW = 8.834 HW1 = 0.583 HW2 = 0.583 And then used g_density ... -ei electrons.dat -dens electron ... There are several problems. The first line of electrons.dat indicates there are only two unique atom names, but clearly you're supplying three. Second, this file is read in such that at integral number of electrons is detected on each line. So, in your case, two lines are being read, one that detects 8 electrons, and another that detects zero. -Justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Tesla S2050 issues
Hi all, I have had no issues compiling OpenMM 2.0 and Gromacs 4.5.x (I have tried all flavors between 1 and 4), but once it comes time to execute mdrun I get the following error message: Error: invalid argument launching kernel kReduceForces The OpenMM group has been helpful in giving suggestions as to what to try, but I am at a loss now. I still get the same error. I have Cuda 3.1 on board and I have been able to compile both OpenMM 2 and OpenMM 3 without issue. I am also able to compile Gromacs, all recent flavors, linking in OpenMM without issue. I have also tried using the stock OpenMM libraries and have ended at the same place. Obviously I get a different error on exit when I link in OpenMM 3, Is it that my card is double precision? Thanks, Matt -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] solvent implicit error
Hi All I am trying analyze the dynamics of polymer of GlcN residues using ffG53a6 force field. I included in toplogy file the follow sentence: ;Include GB Parameters [ implicit_genborn_params ] #include mypath/MYgbsa.itp The MYgbsa.itp is : ; atype sar st pi gbr hct CH1 0.18 1 1.2760.190 0.72 ; C CH2 0.18 1 1.2760.190 0.72 ; C H0.1 1 10.115 0.85 ; H N0.1551 1.0280.17063 0.79 ; N OA 0.15 1 0.9260.148 0.85 ; O When I run grompp I have this error: --- Program grompp, VERSION 4.5.3 Source code file: topio.c, line: 660 Fatal error: Syntax error - File test.top, line 12325 Last line read: '[ implicit_genborn_params ]' Invalid order for directive implicit_genborn_params For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Any help would be appreciated Carmen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_velacc
Hello, I have calculated the velocity autocorrelation function of OH bond in glucose molecule. For this calculation I modified the index file. The modified part is pasted below. [ O10 ] 10 20 10 is oxygen no. and 20 is oxygen. I used following command to calculate the velocity autocorrelation function. g_velacc -f 6.trr -s 6.tpr -n index.ndx -e 100 -nonormalize -o My question is how does the prog. calculate the velocity autocorrlation function. Does is subtract the velocity of hydrogen from oxygen and then calculate the autocorrelation function? I am using gromacs version 4.0.7. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Error of installing gromacs v4.5.4
Hi, That compiler is ancient (thought it might have SSE2 support) as well as the OS, I guess (RHEL 3?). Still, the CPU does support SSE2 so if you can get a gcc 4.1 or later on it you should still be able compile and run the code without a problem. -- Szilárd 2011/5/26 Hsin-Lin Chiang jian...@phys.sinica.edu.tw: Hi, Thank you for your reply. I'm not so good in computer. I think the platform you ask me is Linux, and kernel is 2.4.21-60.ELsmp The compiler is gcc v3.2.3 in the machine in my institute. Sincerely yours, Hsin-Lin Message: 1 Date: Thu, 26 May 2011 18:03:09 +0200 From: Szil?rd P?ll szilard.p...@cbr.su.se Subject: Re: [gmx-users] Error of installing gromacs v4.5.4 To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: BANLkTi=9v3+1dnbjsmd6hna-ayfdprb...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi Hsin-Lin, Your problem are caused by a missing header file which is included by the nobonded SSE kernels which is indicated by the first error in your output: nb_kernel400_ia32_sse.c:22:23: emmintrin.h: No such file or directory This header is needed for SSE and SSE2, but for some reason you don't have it. What platform are you compiling on/for and what compiler are you using? Alternatively, you can turn off acceleration and you'll be able to compile the code, but it will run *much* slower than with the accelerated kernels. -- Szil嫫d -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Domain Motion = How do get the rotational axis from eigenvectors ?
Hi I want to protein's domain motion. I use g_covarandg_anaeig to get the eigenvectors. How can i get the rotational axis of which protein do its domain motion from those eigenvectors? I found the papers and the authors plot its rotational axis of domain motion. How did they make it ? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Domain Motion = How do get the rotational axis from eigenvectors ?
Hi Lin, You don't get such axes directly from covariance analysis. If you want to know which rotations are associated with a certain eigenvector, you have to run a routine like dyndom (http://fizz.cmp.uea.ac.uk/dyndom/) on the extreme projections of your trajectory onto an eigenvector. Cheers, Tsjerk On Fri, May 27, 2011 at 4:54 AM, Chih-Ying Lin chihying2...@gmail.com wrote: Hi I want to protein's domain motion. I use g_covar and g_anaeig to get the eigenvectors. How can i get the rotational axis of which protein do its domain motion from those eigenvectors? I found the papers and the authors plot its rotational axis of domain motion. How did they make it ? Thank you Lin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] problem using trjconv command
Hi all . I am using trjconv command to genrate the pdb structures.. trjconv_d -f md_0_1.trr -s md_0_1.tpr -o md_0_1.pdb -nice 0 -sep -skip 1000 -tu ns -b 1 -e 5000 error is comingFatal error: reading tpx file (md_0_1.tpr) version 73 with version 58 program. what is meaning of this error and what would be the possible solution 2 solve this? -- [image: images[12]] “Many Smiles Begin Because Of Another Smile . . . . Regards, Rashi image004.jpg-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] problem using trjconv command
On 27/05/11, rashi parihar rashi.pari...@gmail.com wrote: Hi all . I am using trjconv command to genrate the pdb structures.. trjconv_d -f md_0_1.trr -s md_0_1.tpr -o md_0_1.pdb -nice 0 -sep -skip 1000 -tu ns -b 1 -e 5000 error is comingFatal error: reading tpx file (md_0_1.tpr) version 73 with version 58 program. what is meaning of this error and what would be the possible solution 2 solve this? You're reading a .tpr file written with a more recent version of GROMACS than the version of trjconv you are using. Because the file formats change as time passes, old code cannot always correctly interpret new data. You should judge either to make a .tpr in the old format, use a file in a different format for -s, or do your analysis with the new code. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
